6ZO7 | pdb_00006zo7

3-Formylrifamycin SV binding to the access pocket of AcrB-G619P L and T protomer

• PDB DOI: https://doi.org/10.2210/pdb6ZO7/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli K-12, synthetic construct
• Expression System: Escherichia coli BL21(DE3), Escherichia coli K-12
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2020-07-07 Released: 2021-05-19 
• Deposition Author(s): Tam, H.K., Foong, W.E., Pos, K.M.
• Funding Organization(s): German Research Foundation (DFG), German-Israeli Foundation for Research and Development, European Communitys Seventh Framework Programme

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.271 (Depositor), 0.268 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 
  0.240 (Depositor) 

Starting Model: experimental

Literature

Allosteric drug transport mechanism of multidrug transporter AcrB.

Tam, H.K., Foong, W.E., Oswald, C., Herrmann, A., Zeng, H., Pos, K.M.

(2021) Nat Commun 12: 3889-3889

• PubMed: 34188038 
• DOI: https://doi.org/10.1038/s41467-021-24151-3
• Primary Citation Related Structures: 
  6ZO5, 6ZO6, 6ZO7, 6ZO8, 6ZO9, 6ZOA, 6ZOB, 6ZOC, 6ZOD, 6ZOE, 6ZOF, 6ZOG, 6ZOH


• PubMed Abstract: 
  

  Gram-negative bacteria maintain an intrinsic resistance mechanism against entry of noxious compounds by utilizing highly efficient efflux pumps. The E. coli AcrAB-TolC drug efflux pump contains the inner membrane H ⁺ /drug antiporter AcrB comprising three functionally interdependent protomers, cycling consecutively through the loose (L), tight (T) and open (O) state during cooperative catalysis. Here, we present 13 X-ray structures of AcrB in intermediate states of the transport cycle. Structure-based mutational analysis combined with drug susceptibility assays indicate that drugs are guided through dedicated transport channels toward the drug binding pockets. A co-structure obtained in the combined presence of erythromycin, linezolid, oxacillin and fusidic acid shows binding of fusidic acid deeply inside the T protomer transmembrane domain. Thiol cross-link substrate protection assays indicate that this transmembrane domain-binding site can also accommodate oxacillin or novobiocin but not erythromycin or linezolid. AcrB-mediated drug transport is suggested to be allosterically modulated in presence of multiple drugs.

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Organizational Affiliation: 
• Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany. [e-mail].
Hengyang Medical College, University of South China, Hengyang, Hunan Province, China. [e-mail].
Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany.
Sosei Heptares, Steinmetz Building, Granta Park, Great Abington, Cambridge, UK.
Institute of Biochemistry, Goethe-University Frankfurt, Frankfurt am Main, Germany. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A3B2 Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Local Symmetry: Cyclic - C3  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 390.91 kDa 
• Atom Count: 26,893 
• Modeled Residue Count: 3,406 
• Deposited Residue Count: 3,509 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Multidrug efflux pump subunit AcrB	A, B, C	1,057	Escherichia coli K-12	Mutation(s): 0  Gene Names: acrB, acrE, b0462, JW0451 Membrane Entity: Yes
UniProt
Find proteins for P31224 (Escherichia coli (strain K12)) Explore P31224  Go to UniProtKB:  P31224

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPIN	D, E	169	synthetic construct	Mutation(s): 0  Gene Names: ARTIFICIAL GENE

Small Molecules

Ligands 13 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTY	CA [auth C], X [auth C]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
3YI (Subject of Investigation/LOI)	N [auth A], V [auth B]	(2S,12Z,14E,16S,17S,18R,19R,20R,21S,22R,23S,24E)-8-formyl-5,6,9,17,19-pentahydroxy-23-methoxy-2,4,12,16,18,20,22-heptam ethyl-1,11-dioxo-1,2-dihydro-2,7-(epoxypentadeca[1,11,13]trienoimino)naphtho[2,1-b]furan-21-yl acetate C38 H47 N O13 BBNQHOMJRFAQBN-UPZFVJMDSA-N
LMT	BA [auth C], F [auth A], G [auth A], H [auth A], IA [auth C], K [auth A], O [auth A], Q [auth B], T [auth B], Y [auth C]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
R16	DA [auth C]	HEXADECANE C16 H34 DCAYPVUWAIABOU-UHFFFAOYSA-N
DDQ	HA [auth C]	DECYLAMINE-N,N-DIMETHYL-N-OXIDE C12 H27 N O ZRKZFNZPJKEWPC-UHFFFAOYSA-N
D12	AA [auth C], Z [auth C]	DODECANE C12 H26 SNRUBQQJIBEYMU-UHFFFAOYSA-N
D10	I [auth A]	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
SO4	W [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	GA [auth C], LA [auth E], R [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
HEX	S [auth B]	HEXANE C6 H14 VLKZOEOYAKHREP-UHFFFAOYSA-N
EDO	FA [auth C], J [auth A], JA [auth C], L [auth A], M [auth A], MA [auth E], P [auth A], U [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	EA [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	KA [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.271 (Depositor), 0.268 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.239 (DCC) 
• R-Value Observed: 0.240 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 144.732	α = 90
b = 157.683	β = 90
c = 244.044	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-05-19 
Deposition Author(s): Tam, H.K., Foong, W.E., Pos, K.M.

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Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	DFG-EXC115
German-Israeli Foundation for Research and Development	Germany	I-1202-248.9/2012
European Communitys Seventh Framework Programme	European Union	FP7/2007-2013

Revision History  

• Version 1.0: 2021-05-19
  Type: Initial release
  
• Version 1.1: 2021-07-07
  Changes: Database references
• Version 1.2: 2021-07-14
  Changes: Database references
• Version 1.3: 2024-01-31
  Changes: Data collection, Database references, Refinement description